Congressional investigators are baffled by the turn of events in the Michael Flynn case. But they know they find the Flynn case troubling, from start to finish. (AP)

In March 2017, then-FBI Director James Comey briefed a number of Capitol Hill lawmakers on the Trump-Russia investigation. One topic of intense interest was the case of Michael Flynn, the Trump White House national security adviser who resigned under pressure on Feb. 13 after just 24 days in the job.

There were widespread reports that Flynn had lied to Vice President Mike Pence about telephone conversations that he, Flynn, had with Russian Ambassador Sergey Kislyak during the transition in late December 2016. On Jan. 24, 2017, two of Comey's FBI agents went to the White House to question Flynn, and there was a lot of speculation later that Flynn lied in that interview, which would be a serious crime.

"The Jan. 24 interview potentially puts Flynn in legal jeopardy," the Washington Post reported in February. "Lying to the FBI is a felony offense."

There was also a lot of concern in Congress, at least among Republicans, about the leak of the wiretapped Flynn-Kislyak conversation. Such intelligence is classified at the highest level of secrecy, yet someone — Republicans suspected Obama appointees in the Justice Department and intelligence community — revealed it to the press.

So in March, lawmakers wanted Comey to tell them what was up. And what they heard from the director did not match what they were hearing in the media.

According to two sources familiar with the meetings, Comey told lawmakers that the FBI agents who interviewed Flynn did not believe that Flynn had lied to them, or that any inaccuracies in his answers were intentional. As a result, some of those in attendance came away with the impression that Flynn would not be charged with a crime pertaining to the Jan. 24 interview.

Nine months later, with Comey gone and special counsel Robert Mueller in charge of the Trump-Russia investigation, Flynn pleaded guilty to one count of making false statements to the FBI in that Jan. 24 questioning.

What happened? With Flynn awaiting sentencing — that was recently delayed until at least May — some lawmakers are trying to figure out what occurred between the time Comey told Congress the FBI did not believe Flynn lied and the time, several months later, when Flynn pleaded guilty to just that.

None of those congressional investigators has an answer; they're baffled by the turn of events. But they know they find the Flynn case troubling, from start to finish.

The questioning in that Jan. 24 interview apparently revolved around the Flynn-Kislyak phone conversations. The first thing to remember is that it appears Flynn did nothing wrong in having those talks. As the incoming national security adviser, it was entirely reasonable that he discuss policy with representatives of other governments — and Flynn was getting calls from all around the world.

So even if Flynn discussed the hot issue of U.S. sanctions against Russia with Kislyak, that was OK. "I don't have a problem with that," former Bush national security adviser Stephen Hadley said in February 2017. "I don't see what would be wrong if [Flynn] simply said, look, don't retaliate, doesn't make sense, it hurts my country, it makes it harder for us as an incoming administration to reconsider Russia policy, which is something we said we'd do. So just hold your fire and let us have a shot at this."

Indeed, it appears the FBI did not think Flynn had done anything wrong in the calls. On Jan. 23, the Washington Post reported that the FBI had reviewed the Flynn-Kislyak calls and "has not found any evidence of wrongdoing or illicit ties to the Russian government." (The calls had been intercepted by U.S. intelligence because the U.S. monitored the Russian ambassador's communications — something which Flynn, a former chief of the Defense Intelligence Agency, surely knew.)

Still, Flynn's conversation had the attention of the Obama Justice Department, and in particular of deputy attorney general Sally Yates, who reportedly believed Flynn might have violated the Logan Act, a 218 year-old law under which no one had ever been successfully prosecuted. (Two people were charged in the 19th century, but the cases were dropped.)

Despite the high level of classification, word of the Justice Department's concerns got to the press. On Jan. 12, Washington Post columnist David Ignatius reported that Flynn and Kislyak had talked. "What did Flynn say, and did it undercut U.S. sanctions?" Ignatius asked. "The Logan Act (though never enforced) bars U.S. citizens from correspondence intending to influence a foreign government about 'disputes' with the United States. Was its spirit violated?"

Three days later, on Jan. 15, Vice President-elect Mike Pence (remember, this was all happening before the Trump administration took office) denied that Flynn had discussed sanctions with the Russian ambassador. "They [Flynn and Kislyak] did not discuss anything having to do with the United States' decision to expel diplomats or impose censure against Russia," Pence told CBS.

On Jan. 20, Donald Trump became president. On Jan. 22, the Wall Street Journal reported that "U.S. counterintelligence agents have investigated communications" between Flynn and Kislyak. The investigation "aimed to determine the nature of Mr. Flynn's contact with Russian officials and whether such contacts may have violated laws."

On Jan. 24, the Justice Department — the Obama holdover Yates had become the acting attorney general — sent two FBI agents to the White House to question Flynn, who talked to them without a lawyer present.

It has sometimes been asked why Flynn, a man long familiar with the ways of Washington, would talk to the FBI without a lawyer. There seems to be no clear answer. On the one hand, as national security adviser, Flynn had plenty of reasons to talk to the FBI, and he could have reasonably thought the meeting would be about a prosaic issue involved in getting the new Trump National Security Council up and running. On the other hand, the media was filled with talk about the investigation into his conversations with Kislyak, and he might just as reasonably have thought that's what the agents wanted to discuss. In any event, Flynn went ahead without an attorney present.

In addition, it appears the FBI did not tell White House officials, including the National Security Council's legal adviser or the White House counsel, that agents were coming to interview the national security adviser over a potentially criminal matter.

Two days later, on Jan. 26, Yates and a high-ranking colleague went to the White House to tell counsel Don McGahn about the Flynn situation. "The first thing we did was to explain to Mr. McGahn that the underlying conduct that Gen. Flynn had engaged in was problematic in and of itself," Yates testified in a May 2017 appearance before a Senate Judiciary Committee subcommittee. That was an apparent reference to the Logan Act, although Yates never specifically said so. "We took him [McGahn] through in a fair amount of detail of the underlying conduct, what Gen. Flynn had done."

Yates then explained to McGahn her theory that Flynn might be vulnerable to blackmail. The idea was that Flynn had discussed sanctions with Kislyak, which of course the Russians knew. And then if Flynn lied to Pence, and Pence made a public statement based on what Flynn had told him, then the Russians might be able to blackmail Flynn because they, the Russians, knew Flynn had not told the vice president the truth.

It was a pretty far-fetched notion, but, along with the never-successfully-prosecuted Logan Act, it was apparently the basis upon which the FBI went inside the White House to do an unannounced interview of a key member of the new administration.

In their discussion, McGahn asked Yates: Even if one White House official lied to another, what's that to the Justice Department? "It was a whole lot more than one White House official lying to another," Yates testified. "First of all, it was the vice president of the United States and the vice president had then gone out and provided that information to the American people who had then been misled and the Russians knew all of this, making Mike Flynn compromised now."

Yates went to see McGahn twice, on Jan. 26 and Jan. 27. On Feb. 13, Flynn resigned. That same day, the Washington Post reported that the Justice Department had pursued Flynn on the grounds of a potential Logan Act violation.

"Yates, then the deputy attorney general, considered Flynn's comments in the intercepted call to be 'highly significant' and 'potentially illegal,' according to an official familiar with her thinking," the Post reported. "Yates and other intelligence officials suspected that Flynn could be in violation of an obscure U.S. statute known as the Logan Act, which bars U.S. citizens from interfering in diplomatic disputes with another country."

On Feb. 14, the New York Times reported that, "Obama advisers grew suspicious that perhaps there had been a secret deal between the incoming [Trump] team and Moscow, which could violate the rarely enforced, two-century-old Logan Act barring private citizens from negotiating with foreign powers in disputes with the United States." (The paper added that the Obama advisers asked the FBI if Flynn and Kislyak had discussed a quid pro quo, only to learn the answer was no.)

At that point, the public still did not know that the Jan. 24 FBI interview of Flynn had taken place. That report came on Feb. 17, when the Washington Post reported the interview in a story headlined, "Flynn told FBI he did not discuss sanctions." That was the piece that noted Flynn was in legal jeopardy, and that, "Lying to the FBI is a felony offense."

Congress, in the meantime, was in the dark about what was going on. Given the intense discussion of the Flynn case in the media, there was no doubt lawmakers were going to want to know what was happening in the Flynn matter, as well as other aspects of the Trump-Russia investigation. (At that point, the FBI had never even publicly acknowledged that there was an investigation into the Trump campaign and Russia.)

So Comey went to Capitol Hill in March to brief lawmakers privately. That is when he told them that the FBI agents who interviewed Flynn did not believe Flynn had lied, or that any inaccuracies in Flynn's answers were intentional. And that is when some lawmakers got the impression that Flynn would not be charged with any crime pertaining to the Jan. 24 interview.

There was still the possibility Flynn could face legal trouble for something else, like failing to register his representation of Turkey. But as far as the question of a "1001 charge" — a charge of lying to investigators, known by its number in the federal code — some lawmakers took that as a sign that Flynn was out of the woods.

On the other hand, the FBI does not make prosecution decisions. (That was not true, of course, in the case of the Clinton email investigation, in which the attorney general effectively gave Comey the decision of whether or not to prosecute.) It could be that the FBI agents who did the questioning were overruled by Justice Department officials who came up with theories like Flynn's alleged violation of the Logan Act or his alleged vulnerability to blackmail.

In any event, much happened after the FBI director's March briefings of Congress. In May, the president fired Comey. The Justice Department, under Trump-appointed deputy attorney general Rod Rosenstein, chose Robert Mueller to be the Trump-Russia special counsel. Mueller gathered a number of prosecutors known for tough, take-no-prisoners tactics. And on Dec. 1, Flynn pleaded guilty to lying to the FBI.

Yates went on to become a heroine of the Trump resistance (and at least one of Mueller's prosecutors) after she refused to enforce the president's travel ban executive order, and Trump summarily fired her. Her legacy lives on in United States v. Michael T. Flynn.

But to outside observers, mystery still surrounds the case. To some Republicans, it appears the Justice Department used a never-enforced law and a convoluted theory as a pretext to question Flynn — and then, when FBI questioners came away believing Flynn had not lied to them, forged ahead with a false-statements prosecution anyway. The Flynn matter is at the very heart of the Trump-Russia affair, and there is still a lot to learn about it.